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- PDB-7a80: rsGreen0.7-K206A-E222V in the green-on state -

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Basic information

Entry
Database: PDB / ID: 7a80
TitlersGreen0.7-K206A-E222V in the green-on state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Reversible photoswitchable fluorescent protein
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / NITRATE ION / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsDe Zitter, E. / Dedecker, P. / Van Meervelt, L.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders Belgium
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System*.
Authors: De Zitter, E. / Hugelier, S. / Duwe, S. / Vandenberg, W. / Tebo, A.G. / Van Meervelt, L. / Dedecker, P.
History
DepositionAug 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5738
Polymers122,3254
Non-polymers2484
Water10,485582
1
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6432
Polymers30,5811
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6432
Polymers30,5811
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6432
Polymers30,5811
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6432
Polymers30,5811
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.822, 61.800, 112.121
Angle α, β, γ (deg.)90.000, 91.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Green fluorescent protein


Mass: 30581.354 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli (E. coli) / Variant (production host): JM109 / References: UniProt: A0A059PIQ0
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 26 % PEG 4000 500 mM Mg(NO3) 50 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.05→46.27 Å / Num. obs: 60229 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 27.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.041 / Rrim(I) all: 0.105 / Net I/σ(I): 13.2 / Num. measured all: 405037
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.16.90.6823041544240.8610.2820.7392.9100
9.17-46.275.60.04939987150.9970.0220.0542898.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.62 Å46.27 Å
Translation5.62 Å46.27 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→46.274 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 3006 4.99 %
Rwork0.1829 57196 -
obs0.1854 60202 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.03 Å2 / Biso mean: 29.6827 Å2 / Biso min: 11.64 Å2
Refinement stepCycle: final / Resolution: 2.05→46.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7207 0 16 582 7805
Biso mean--37.64 35.69 -
Num. residues----909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027680
X-RAY DIFFRACTIONf_angle_d0.55710438
X-RAY DIFFRACTIONf_chiral_restr0.0461123
X-RAY DIFFRACTIONf_plane_restr0.0031382
X-RAY DIFFRACTIONf_dihedral_angle_d10.1336161
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.08360.34841230.269427292852100
2.0836-2.11960.35571160.264727682884100
2.1196-2.15810.28391490.245926652814100
2.1581-2.19960.31261500.244426822832100
2.1996-2.24450.31751570.220626942851100
2.2445-2.29330.22671730.186826952868100
2.2933-2.34670.2721540.18526782832100
2.3467-2.40540.25271580.187327072865100
2.4054-2.47040.28581510.19626982849100
2.4704-2.54310.28661240.192827252849100
2.5431-2.62520.22671710.191426692840100
2.6252-2.7190.24641360.190127312867100
2.719-2.82780.24491220.191127682890100
2.8278-2.95650.26081260.199627162842100
2.9565-3.11230.25091350.187427472882100
3.1123-3.30730.22081280.17727302858100
3.3073-3.56260.23021680.176327002868100
3.5626-3.92090.21731470.164327402887100
3.9209-4.48790.15831280.147127562884100
4.4879-5.65260.1841370.147927832920100
5.6526-46.28530.23261530.19012815296899

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